New Jersey is "getting to a point now where the actual remaining number is extremely low," said principal zoologist Mick Valent of the New Jersey Department of Environmental Protection's Division of Fish and Wildlife.
The state has been nursing some infected bats back to health and plans to release them soon.
Pennsylvania also has suffered "significant devastation to the bat populations," said Travis Lau, a spokesman for the Pennsylvania Game Commission.
The state has been trying - so far unsuccessfully - to develop a treatment for white-nose syndrome, which spreads as fuzzy spots across the bats' muzzles, ears, and wings.
The fungus causes discomfort and saps fat reserves over the winter, prematurely awakening bats from hibernation to hunt for food and eventually die of starvation.
It was apparently brought to the United States from Europe, though it's not clear whether it came over on an affected bat or the gear of a cave explorer.
First seen near Albany, N.Y., in February 2006, white-nose syndrome moved on to New England, north to Ontario, west to Oklahoma, Missouri, and Minnesota, and south to Georgia, Alabama, and Arkansas.
It appeared in New Jersey and Pennsylvania in 2009 and quickly affected bats across both states, officials said.
In New Jersey, which has about 400 abandoned iron mines, tens of thousands of bats have died. At the former Hibernia mine in Morris County, one of two sites with the largest number of bats, fewer than 500 of 30,000 remain, officials said.
"We monitor 12 to 15 former mines and have found some with less than 50," Valent said. "In others, the populations have completely disappeared."
That's why the state created a "head start program for bats," capturing 10 infected males and 20 infected females to nurse at a facility in Milford, Hunterdon County, Valent said.
They banded all of them and plan to release 20 in the coming days, and will monitor their progress while holding on to 10 females for further study.
In Pennsylvania, which has 2,500 natural caves and 5,000 abandoned mines, Pennsylvania Game Commission officials monitor 60 sites known to have bats.
"We've seen a 90 percent drop in the number of hibernating bats compared to the number prior to 2009, when white-nose syndrome first appeared," Lau said. "The loss is a real cause for concern.
"This mammal is not like a cottontail rabbit," which has many offspring, he said. "It has one or two pups per year."
As a protective measure, officials have installed surveillance cameras at some posted and gated Pennsylvania caves and mines so they can check for trespassers who might disturb the bats and exacerbate problems caused by white-nose syndrome.
"There is too much traffic inside the caves, too many people who shouldn't be there," Lau said. "Some go in to explore; others have illegal automatic weapons and go in there to shoot them.
"The presence of individuals in caves can wake the bats and cause them to fly off" during a time when they're hibernating, he said. "That can cause them to burn stored-up fat and that means they might not make it to the spring."
Some cave-dwelling species, including the northern long-eared bat and the Indiana bat, appear headed for extinction because of white-nose syndrome, according to a 2012 study by ecologists led by researchers at the University of California and Boston University.
In Pennsylvania and New Jersey, little brown bats appear particularly hard hit, possibly because they're most numerous and gather together in cool dark caves where the fungus thrives and can be spread.
Also impacted - though not as greatly - are the less numerous big brown bats, tricolored bats, and eastern small-footed bats. Some hibernate in buildings and other man-made structures instead of caves and mines.
Migratory bats appear unaffected, as they come to the region during warmer months.
They also eat mosquitoes, bugs, and other pests, said Mark O'Neill, a spokesman for the Pennsylvania Farm Bureau. "In addition, there are many birds, including countless barn swallows," that feast on them, too.
Still, farmers "are concerned about the possibility that the situation could cause problems in the future," O'Neill said.
Bats "play a very important role in the environment and ecology because of their consumption of insects," said Jeremy Markuson, a biologist with the New Jersey Field Office of the U.S. Fish and Wildlife Service. With the declining population of some bat species, "you may see more insects than normal," he said.
The loss of millions of bats can only "have a horrible impact," said Amanda Lollar, founder and president of Bat World Sanctuary, a nonprofit bat rescue and conservation group in Weatherford, Texas. "When you have insect damage to the crops, prices will go up in grocery stores."
Farmers will use more pesticides, which can run off into streams, Lollar said.
"Everything is like a giant spiderweb," she said. "When one strand is broken - with bats disappearing - it affects the entire environment."